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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 72, Issue 4

sp. nov., isolated from tidal flat sediment, and emended descriptions of the genus and Free

Abstract

A novel bacterium, designated SCR006, was isolated from tidal flat sediment from Suncheon Bay, Republic of Korea. Cells of strain SCR006 were strictly anaerobic, motile cocci, Gram-reaction-negative, and catalase- and oxidase-negative. Growth was observed at 4–41 °C (optimum, 34–37 °C), at pH 6.5–10.0 (optimum, pH 7.0–7.5) and in presence of 0–8 % NaCl (optimum, 0–2 %). Fermentation products of peptone–yeast–glucose medium were acetate and ethanol. Results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SCR006 had high sequence similarity to D3RC-2 (97.9 %), followed by DSM 6139 (95.9 %) and 232.1 (95.0 %). The average nucleotide identity value between strain SCR006 and DSM 24773 was 72.7 %, which strongly supported that strain SCR006 reresents a novel species within the genus . The major cellular fatty acids are iso-C (27.2 %) and anteiso-C (16.9 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unidentified phospholipids, an unidentified aminolipid and five unidentified lipids. The genomic size was 3.2 Mb with genomic DNA G+C content of 45.6 mol%. The results of 16S rRNA-based and genome-based phylogenetic tree analyses indicated that SCR006 should be assigned to the genus . Strain SCR006 could be distinguished from D3RC-2 by its growth conditions, cell morphology and genomic characteristics. Based on the phenotypic, phylogenetic, genomic and chemotaxonomic features, strain SCR006 represents a novel species, for which the name sp. nov. is proposed, with the type strain SCR006 (=KCTC 25245= JCM 34531)

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Keyword(s): Proteiniclasticum aestuarii sp. nov. , Suncheon Bay and tidal flat
© 2022 The Authors
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2022-04-08
2025-04-28
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References

  1. Lee TK, Lee J, Sul WJ, Iwai S, Chai B et al. Novel biphenyl-oxidizing bacteria and dioxygenase genes from a korean tidal mudflat. Appl Environ Microbiol 2011; 77:3888–3891 [View Article] [PubMed]
     [Google Scholar]
  2. Chun J-S, Kim B-S, Oh H-M, Kang H-J, Park S-S. Remarkable bacterial diversity in the tidal flat sediment as revealed by 16S rDNA analysis. J Microbiol Biotechnol 2004; 14:205–211
     [Google Scholar]
  3. Choi HJ, Jeong T-Y, Yoon H, Oh BY, Han YS et al. Comparative microbial communities in tidal flats sediment on Incheon, South Korea. J Gen Appl Microbiol 2007; 2018:2017
     [Google Scholar]
  4. Yang Y, Liu C-T. Distribution of nitrogen components in seawater overlying the Gomso tidal flat, The Sea. J Oceanogr 2003; 59:251–257 [View Article]
     [Google Scholar]
  5. Hu Y, Wang L, Tang Y, Li Y, Chen J et al. Variability in soil microbial community and activity between coastal and riparian wetlands in the Yangtze River estuary – Potential impacts on carbon sequestration. Soil Biol Biochem 2014; 70:221–228 [View Article]
     [Google Scholar]
  6. Azam F, Worden AZ. Oceanography. Microbes, molecules, and marine ecosystems. Science 2004; 303:1622–1624 [View Article] [PubMed]
     [Google Scholar]
  7. Ludwig W, Schleifer K-H, Whitman WB. Revised road map to the phylum Firmicutes. In Bergey’s Manual® of Systematic Bacteriology New York: Springer; 2009 pp 1–13
     [Google Scholar]
  8. Zhang K, Song L, Dong X. Proteiniclasticum ruminis gen. Int J Syst Evol Microbiol 2010; 60:2221–2225 [View Article]
     [Google Scholar]
  9. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article] [PubMed]
     [Google Scholar]
  10. Namirimu T, Park M-J, Yang S-H, Zo Y-G, Kwon KK. Parashewanella tropica sp. nov., a mesophilic bacterium isolated from a marine sponge from Chuuk lagoon, Federated States of Micronesia, and emended description of the genus Parashewanella. Int J Syst Evol Microbiol 2019; 69:3256–3261 [View Article] [PubMed]
     [Google Scholar]
  11. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article] [PubMed]
     [Google Scholar]
  12. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  13. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
     [Google Scholar]
  14. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  15. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
     [Google Scholar]
  16. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  17. Kimura M. The neutral theory and molecular evolution. In My Thoughts on Biological Evolution Singapore: Springer; 2020 pp 119–138
     [Google Scholar]
  18. Lawson PA, Wawrik B, Allen TD, Johnson CN, Marks CR et al. Youngiibacter fragilis gen. nov., sp. nov., isolated from natural gas production-water and reclassification of Acetivibrio multivorans as Youngiibacter multivorans comb. nov. Int J Syst Evol Microbiol 2014; 64:198–205 [View Article]
     [Google Scholar]
  19. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
     [Google Scholar]
  20. Stackebrandt E. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
     [Google Scholar]
  21. Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A et al. Assembling genomes and mini-metagenomes from highly chimeric reads. In Annual International Conference on Research in Computational Molecular Biology Berlin, Heidelberg: Springer; 2013 pp 158–170 [View Article]
     [Google Scholar]
  22. Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 2016; 44:D286–93 [View Article] [PubMed]
     [Google Scholar]
  23. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
     [Google Scholar]
  24. Lee MD. GToTree: a user-friendly workflow for phylogenomics. Bioinformatics 2019; 35:4162–4164 [View Article] [PubMed]
     [Google Scholar]
  25. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
     [Google Scholar]
  26. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  27. Xu L, Dong Z, Fang L, Luo Y, Wei Z et al. OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 2019; 47:W52–W58 [View Article] [PubMed]
     [Google Scholar]
  28. Muneyuki E, Noji H, Amano T, Masaike T, Yoshida M. F(0)F(1)-ATP synthase: general structural features of “ATP-engine” and a problem on free energy transduction. Biochim Biophys Acta 2000; 1458:467–481 [View Article] [PubMed]
     [Google Scholar]
  29. Skulachev VP, Bogachev A. Membrane Bioenergetics Berlin: Springer-Verlag; 1988 pp 232–246 [View Article]
     [Google Scholar]
  30. Mulkidjanian AY, Galperin MY, Makarova KS, Wolf YI, Koonin EV. Evolutionary primacy of sodium bioenergetics. Biol Direct 2008; 3:1–9 [View Article] [PubMed]
     [Google Scholar]
  31. Ozawa K, Meikari T, Motohashi K, Yoshida M, Akutsu H. Evidence for the presence of an F-type ATP synthase involved in sulfate respiration in Desulfovibrio vulgaris. J Bacteriol 2000; 182:2200–2206 [View Article] [PubMed]
     [Google Scholar]
  32. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  33. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
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Proteiniclasticum aestuarii sp. nov., isolated from tidal flat sediment, and emended descriptions of the genus Proteiniclasticum and Proteiniclasticum ruminis
Int J Syst Evol Microbiol 72, 005275 (2022); https://doi.org/10.1099/ijsem.0.005275
/content/journal/ijsem/10.1099/ijsem.0.005275
/content/journal/ijsem/10.1099/ijsem.0.005275
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